The visitors travelled north after three wins and a solitary loss to Celtic and swept into the lead after only three minutes. Home skipper Lyall Booth appeared to be impeded in the build up freeing space for Thomson to run on to Struthers' cross and fire past Shingler.
Aberdeen responded well to the setback, enjoying the lion's share of possession but they were unable to penetrate a well-drilled Saints defence. A foul on Dangana led to centre back Kenny being booked on 20 minutes before a well-worked corner by McMaster and the impressive Taylor saw the former force a neat save from Shingler.
Despite a torrential downpour and hailstones, both teams were playing some very attractive football.
Ryan Duncan showed his class on 25 minutes driving forward through midfield. The youngster from Keig exchanged passes with Dangana before his well-struck shot was saved at the second attempt by the keeper. A minute later the Buddies burst forward after a Dons corner had been cleared and Thomson went down in the box under pressure from Buchan, but to the visitors' dismay, the ref decided he had dived and showed a yellow card.
Approaching the half hour Aberdeen were really pushing for parity and Duncan's rocket shot flew inches wide before Kennedy saved well with his feet to deny Adam Emslie. The young Dons were by now playing some excellent passing football, really moving the ball well at speed.
Despite more pressure from the Dons, the young Buddies held on until the break to go in one up at the changeround.
Half time - Aberdeen Under 18s 0 St Mirren Under 18s 1
Dons coach Scott Anderson made a change on 56 minutes, Liam Harvey coming on for Tom Findlay.
Moments later Michael Dangana was the second player cautioned for simulation. Just before thew hour mark it was all square as MacIver's left wing corner was bundled into the net by the towering Jack Milne - no more than the Dons deserved.
Three minutes later major controversy as the Dons had the ball in the net after another excellent corner from Jack MacIver. Ryan Duncan's final touch appeared to come after the ball had broken to him off a St Mirren defender on the line but an offside flag from the dugout side linesman cut the celebrations short.
The decision was to have a major bearing on the outcome of the game.
In the 70th minute the officials were in the spotlight again as St Mirren took the lead for a second time.
As the visitors broke forward there appeared to be a clear push by Thomson to clear himself of the attentions of Lyall Booth and receive the ball in a suspiciously offside position before beating Shingler for a second time. Booth's protest led to him being booked.
Sixty seconds later the Dons were reduced to ten men when skipper Booth hacked Thomson down on the edge of the box, McMaster's resulting free kick crashing off the post to safety.
St Mirren then took control.
On 75 minutes it was 3-1 to the Buddies as a fine Ellis cross deflected off the unfortunate Buchan before nestling in the net. Three minutes later the game was put to bed as substitute McLeish found the net from 20 yards, his low shot beating Shingler.
There was a consolation for the Dons when they completed the scoring on 88 minutes, Dangana converting from the spot after Kenny had been deemed to have fouled him in the box. Possibly a soft award, but Dangana's conversion of the penalty was textbook.
The second goal and the dismissal of Booth allowed Saints a chance to pass the ball around and to their credit they managed the game very well, but Aberdeen will feel very hard done by after dominating large chunks of a match often played in difficult conditions.
This mini campaign is proving to be a major learning curve for the young Dons squad, but one that will certainly help them next season.
On Tuesday, Aberdeen travel to Auchenhowie to face Rangers.